Tandem repeats in big archaeal Borg components endure speedy evolution and create new intrinsically disordered areas in proteins

We reconstructed and manually curated six new Borg genomes to completion (see Strategies; Desk 1). Curation included correction of native errors the place the robotically generated assemblies collapsed areas, or integrated the improper variety of repeat models. These areas have been recognized visually based mostly on elevated incidence of SNPs (Fig 1A) that clearly indicated that the area was misassembled (Fig 1B). All gaps created through the scaffolding step of the meeting have been crammed and genome fragments prolonged by making use of unplaced or misplaced paired reads. In some circumstances, the extending sequences have been used to determine lacking genome fragments that have been then curated into the ultimate meeting. In a number of cases, TR areas exceeded the sequencing insert size so the actual variety of TR models couldn’t be exactly decided. Resolving the de novo meeting errors unmasked TR areas within the genomes and revealed the aaTRs that these introduce into protein sequences.

Fig 1. Reads mapped to a de novo meeting earlier than and after curation.

Reads are proven as gray bars beneath the consensus sequence. SNPs in reads are highlighted in coloration. The pink segments mark a singular sequence that was used to position misplaced reads accurately and the nucleotide repeat unit is proven as black segments. (A) Numerous SNPs signifies a neighborhood meeting error related to a collapsed repeat area, leading to a consensus sequence with one repeat unit. (B) The consensus sequence has three repeat models after curation.

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Rose Borg possesses the smallest (623,782 bp), and Inexperienced Borg possesses the most important genome (1,094,519 bp). As anticipated, based mostly on the 4 beforehand reported genomes, 5 of the brand new genomes are linear, terminated by inverted repeats. Based mostly on GC skew evaluation, replication of Borg DNA is initiated on the chromosome ends (Figs 2 and S1 and S1 Desk). The Pink Borg genome accommodates a repeated sequence that prevented identification of a singular genome meeting path. The variant that generated the anticipated sample of GC skew as for the opposite Borgs was chosen, finishing the ultimate set of ten Borg genomes. All genomes however the Inexperienced Borg genome are composed of a giant and a small replichore; the Inexperienced Borg genome has a barely extra advanced group. Every replichore carries primarily all genes solely on one strand. Consequently, there are not any obvious transcriptional operons. This was mirrored by a low frequency of transcriptional regulators in Borg genomes. Particularly, we solely discovered 0.35 transcriptional regulators per 100 kbp Borg genome, whereas close to full Methanoperedens genomes encoded 5.9 in 100 kbp (1 in Rose; 2 in Purple; 3 in Brown, Lilac, Sky, Inexperienced; 5 in Purple; 6 in Orange; and none in Ochre and Pink Borg versus 53, 53, and 62 in three near-complete Methanoperedens genomes SRVP18_hole-7m-from-trench_1_20cm__Methanoperedens-related_44_31,RifSed_csp2_16ft_3_Methanoperedens_45_12,RifSed_csp1_19ft_2_Methanoperedens_44_10; 2.77–2.90 Mbp). We additionally observe that not one of the Borgs encode a DNA-dependent RNA polymerase or a TATA-box binding protein.

Fig 2. Borg genomes are composed of a giant and a small replichore, and their replication is initiated on the termini.

Proven is the genome structure of Brown Borg, together with terminal inverted repeats (white arrows), TR areas (purple arrows), and GC composition. GC skew and cumulative GC skew present that the genome is replicated from the terminal inverted repeats (origin) to the terminus. The info underlying this Determine may be present in S1 Desk.

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Within the instance of a repeat area in a MHC gene, there are two TR unit sorts that differ by a G → A substitution SNP that’s synonymous on the amino acid stage. Curiously, the combination of TR variants can differ inside a Borg inhabitants (S2 Fig).

To evaluate whether or not TR areas have been significantly vulnerable to mutation, and, particularly, if there’s a bias towards sure SNPs, we analyzed the reads mapped to every Borg genome utilizing inStrain [11]. We detected no SNPs in 3 genomes and intensely few SNPs in 6 genomes (2.2 SNPs throughout the cumulative TR areas of every genome). The exception was Lilac Borg, which harbored 17 SNPs of which 7 have been inside the similar TR area inside an MHC (S2 Desk). These small numbers preclude any statistical analyses of various mutation incidences within the TR areas in comparison with the entire genome. Curiously, we noticed an A-bias within the SNPs present in TR areas, and that is primarily on the expense of G (14/18 circumstances). In distinction, A-SNPs present in non-TR areas have been equally at the price of G (462/1057 circumstances) and C (494/1057 circumstances), however much less incessantly at the price of T (101/1057 circumstances).

The variety of TR models in a area typically clearly differed inside a single Borg inhabitants (Fig 3A). This suggests that the Borg TR areas are quick evolving, very similar to CRISPR repeat-spacer inventories. Furthermore, the repeat loci have been hardly ever conserved in in any other case alignable areas of probably the most intently associated Borgs and have been absent from homologous proteins from the host or different homologues in NCBI or our personal database ggKbase. That is further proof that TR areas shaped very not too long ago, after Borgs diverged. A uncommon case the place TR areas are comparable happens in Black and Brown Borgs, that are intently associated based mostly on genome alignments (Fig 3B). Shut inspection of an roughly 7-kbp area within the aligned genomes revealed an 83% sequence identification and 4 totally different sorts of TRs. TR-1 is intergenic, consists of a 20-nt unit repeated six instances, adopted by an almost good further unit of 21 nt, then one other good unit. This intergenic TR is absent in Brown Borg. TR-2 is in an ORF and includes 18 nt models which might be equivalent in Black and Brown Borgs, the place they happen seven and eight instances, respectively. TR-3 can also be in an ORF and includes 21 nt models that happen consecutively six instances in Black Borg. Brown Borg has two equivalent models in the identical ORF, adopted by a sequence that differs by one SNP, then one other equivalent unit. TR-4 can also be in an ORF and includes 36 nt models that happen 4 instances in Brown Borg, however these are absent in the identical ORF from Black Borg. Curiously, the nucleotide sequence from Brown Borg within the neighborhood of TR-4 has excessive nucleotide-level similarity however no TRs.

Fig 3. Variability of TR unit numbers inside one Borg inhabitants and variations in TR areas in two intently associated however distinct Borg genomes.

(A) The consensus sequence of the reads mapped to the curated genome accommodates three TR models (aqua segments). Reads are proven as gray bars beneath the consensus sequence (***). Six reads span this area completely (**), 5 reads span this area however are lacking one TR unit (*, black segments), 9 reads don’t span your entire TR area. (B) Genome alignment of intently associated Black Borg and Brown Borg. Genomic areas that align are depicted because the same-colored collinear blocks within the high panel. A 7-kb area (black field) reveals 4 cases of TRs in these genomes: TR-1 is current in Black Borg however absent in Brown Borg; TR-2 is current in each Borg genomes however with totally different numbers of TR models; TR-3 is just current in Black Borg, however an imperfect model is current in Brown Borg; TR-4 is just current in Brown Borg. Similar coloration segments present equivalent TR models; genes are depicted in gray.

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To constrain the mechanism behind TR formation in Borg genomes, we assessed traits of the TR sequences and their flanking DNA areas. Repetition of sequences with variation in GC versus AT content material typically introduces GC/AT-symmetry in areas containing TR models (Fig 4 and S3 Desk). Offset of the symmetric models and the TRs is determined by the precise alternative of the repeat unit. The TR areas may be preceded by sequences which might be equivalent to the tip of the TR unit and/or adopted by sequences which might be equivalent to the beginning of the TR unit (Fig 4A and 4B). These flanking partial repeats are sometimes additionally adjoining to TR areas that include solely two repeats (and have been excluded from statistics). Usually the center of the TR unit shouldn’t be in both of the 5′ or 3′ partial repeats. When there are totally different decisions for the repeat unit there are barely totally different partial repeats that flank the TR sequences (Fig 4C).

Fig 4. Tandem repeats are sometimes flanked by partial repeat sequences.

(A) TR areas can happen inside ORFs. (B) TRs may be in intergenic areas, or the area can begin inside the finish of an ORF. The TR areas are sometimes flanked by partial repeats. (C) Completely different choices for the beginning of a TR area outline totally different flanking partial repeats. The GC graph shows the proportional quantity of G or C (or A or T) residues in a sliding window that’s set at half of the TR unit size. The info underlying this Determine may be present in S3 Desk.

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The nucleotide composition of the ORF-carrying strands on each replichores was comparable, with nucleotide frequencies of A>T>G>C (38.4%, 28.8%, 20.3%, 12.5%). The nucleotide composition of all TR models in comparison with this total composition confirmed a powerful bias in direction of A (48.4%), whereas all different nucleotides have been depleted (T 23.7%, G 17.1%, C 10.8%) (S4 Desk). This A-bias is analogous to the A-bias noticed in SNPs inside TR areas (S2 Desk). To determine that the variations in nucleotide composition of the TRs versus all nucleotides are important, we carried out a nonparametric Kruskal–Wallis check [12] and a false discovery fee (FDR) correction in line with Benjamini–Yekutieli [13]. This revealed that the compositional bias between the nucleotide TRs and non-TR sequences is of excessive statistical significance with corrected p-values of 9.78 × 10⁻⁶⁸, 1.95 × 10⁻⁴¹, 1.46 × 10⁻²⁹, 1.51 × 10⁻²³ for A, T, G, C. This bias was much less pronounced in TRs inside ORFs (A 46.3%), and these TRs have been additionally enriched in C (15.5%), whereas T and G have been depleted (18.6%, 19.6%) (corrected p-values of 1.39 × 10⁻¹⁸, 5.06 × 10⁻⁵⁸, 8.40 × 10⁻³, 2.16 × 10⁻³ for A, T, G, C) (S4 Desk). The truth that this compositional bias is noticed in each genes, intergenic areas and in flanking partial repeats means that the A enrichment is essential for the method that kinds the repeats. Predicting the RNA secondary construction of the nucleotide TRs with RNAfold [14] revealed that some are predicted to type loops and others type hairpins.

We looked for polymerases in Borg genomes, given their potential relevance for repeat formation [15]. We discovered that each one Borgs encode at the very least one DNA polymerase and phylogenetic placement inside reference sequences [16] revealed that there are two varieties of PolBs encoded within the Borgs: the B2 clade and the B9 clade (S3 Fig). The DNA PolB9 encompasses a predicted 3′ to five′ exonuclease and was present in every full Borg genome. The amino acid sequences are very comparable, suggesting a excessive mode of conservation for these explicit proteins.

To make clear the function and performance of the TRs, we surveyed their prevalence throughout all ten full Borg genomes. We discovered 460 areas that make up 0.62% of the common Borg genome (Desk 1). Draft Methanoperedens metagenomes then again solely have 1 to 4 TR areas, making up ≤0.01% of the metagenomes (0.0099% in SRVP18_hole-7m-from-trench_1_20cm__Methanoperedens-related_44_31, 0.0021% RifSed_csp2_16ft_3_Methanoperedens_45_12, 0.0018% in RifSed_csp1_19ft_2_Methanoperedens_44_10), suggesting that TR formation is extremely genome particular. Roughly half (43% to 65%) of the Borg TRs have been positioned inside ORFs. All TRs inside ORFs had unit lengths which might be divisible by three, so these repeats don’t disrupt studying frames. They lead to amino acid tandem repeats that we consult with as aaTRs (and aaTR-proteins). Solely 14% to 38% of intergenic TR unit lengths have been divisible by three (S4 Fig). Typically, a number of totally different TRs occurred inside the similar ORF, so the dataset comprised 214 aaTRs in 178 particular person proteins from 10 Borg genomes. Fifteen aaTR-proteins weren’t good TRs on the nucleotide stage, but virtually all have been imperfect because of the prevalence of single SNPs. The TR nucleotide sequences are just about all distinctive inside every Borg genome and are very hardly ever shared between Borg genomes, with solely 5 circumstances of equivalent TR models in the identical genome (Inexperienced Borg TR 16 and 19 and TR 17 and 21; S14 Desk) or shared between Borgs (Black Borg TR 35 and Brown Borg TR 31, Black Borg TR 43 and Brown Borg TR 38, Purple Borg TR 21 and Ochre Borg 13). Upon inspection of aaTR-proteins, we discovered a special codon utilization in genes with TRs relative to all Borg genes. As anticipated, based mostly on the comparatively A-rich composition of repeat areas, the aaTR-bearing ORFs typically favored incorporation of codons containing A. Codons containing T in any place have been typically depleted in aaTR areas. Codons with C in place 1 or 2 of the triplett, and G in place 1 have been enriched in aaTRs, however codons with C or G in different positions or mixtures of positions 1 to three have been depleted (S5A Fig and S5 Desk). Probably the most frequent codons in aaTRs have been CCA (encoding proline) and ACA (encoding threonine) with an as much as 3-fold larger frequency in aaTRs than in non-aaTR areas. Probably the most statistically enriched codons in TRs have been GAT and AAA (encoding aspartate and lysine with corrected p-values of 1.63 × 10⁻⁵⁷ and 1.66 × 10⁻⁵²), and most statistically depleted codons in TRs have been ATG and TTT (begin codon and phenylalanine with corrected p-values of 6.43 × 10⁻¹⁰⁴ and 6.67 × 10⁻¹⁰⁰) (S5 Desk). Seven codons have been fully absent in aaTRs, specifically, TGA, TAA, and TAG (cease codons), CGA, CGT, and CGG (encoding arginine), TTC (phenylalanine), and TGC (cysteine) (S5B Fig).

We intently examined the expected biophysical and biochemical properties of the one repeat models from all ten Borg genomes and 37 further proteins from curated Borg contigs. This closing dataset comprised 215 Borg aaTR-proteins and 306 repeat areas (S6 and S7 Tables). Proline, threonine, glutamate, and lysine have been significantly enriched throughout all Borgs, whereas tryptophan, cysteine, and phenylalanine have been virtually absent (Fig 5A and S8 Desk). We seen that disorder-promoting amino acids have been enriched within the aaTRs and order-promoting amino acids have been depleted (S6 Fig).

Fig 5. Relative amino acid abundance in aaTRs and hierarchical clustering of triple aaTR models.

(A) Relative aa abundance in aaTRs in comparison with all proteins. (B) Repeat models have been hierarchically clustered based mostly on triple aaTR models. Clusters with ≥3 aaTR members have been named by amino acids that type the aaTR unit in descending order (threshold ≥10%). The colour strip reveals through which Borg genome every aaTR is encoded. The info underlying this Determine may be present in S7 and S8 Tables.

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Hierarchical clustering of triple aaTR models revealed 28 aaTR clusters, every cluster composed of aaTRs with very comparable amino acid composition and frequency (Fig 5B and S7 Desk). Many aaTR models possessed almost equal numbers of the charged amino acids Ok and E (polyampholyte repeat cluster); others have been enriched in P/T/S, that are potential websites of posttranslational modification. From this, we conclude that there are distinct and associated teams of aaTRs.

To additional examine the remark that aaTRs significantly typically include disorder-promoting amino acids, we assessed the prominence of intrinsically disordered areas (IDRs) in aaTR-proteins versus all Borg proteins. IDRs are polypeptide segments which might be characterised by a scarcity of a well-defined 3D construction [17]. Remarkably, 62.8% aaTR-proteins contained at the very least one IDR (≥15 amino acids), whereas solely 5.6% of all Borg proteins contained an IDR. The relative size of the IDR areas diverse from 2.6% to 100% and 1.2% to 100% in each aaTR-proteins and non-aaTR-proteins (S7 Fig and S9 Desk). In aaTR-proteins, the IDRs virtually at all times corresponded to the TR area, and Methanoperedens homologues didn’t have IDRs (Fig 6A). Thus, we hypothesize that the TRs in ORFs principally result in the creation of recent IDRs in present proteins.

Fig 6. aaTRs introduce intrinsic dysfunction, are predicted binding websites, and comprise comparable amino acids in homologous Borg proteins.

(A) Area structure of S-layer protein from Inexperienced Borg. The aaTR area is intrinsically disordered (predicted with IUPred3; [28]), and the IDR areas are predicted binding websites for proteins, DNA, RNA, or a linker area (predicted with flDPnn [60]; likelihood of function will increase with coloration depth). (B) All or most members of two protein subfamilies have aaTRs. The aaTRs inside a protein subfamily are from one or two associated aaTR clusters. The amino acid sequence of every aaTR unit is proven in brackets.

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Forty proteins possessed a number of repeat areas starting from two to 5 aaTR areas (S10 Desk), and the aaTRs have been typically positioned on the N- or C-termini or between domains. A few of these areas fall into the identical or the same aaTR cluster, whereas others are distinct and infrequently positioned in a totally totally different area of the polypeptide chain. In 22 circumstances, the aaTRs make up the bulk (50% to 96%) of the expected proteins, and lots of of those are small proteins (14 proteins are <100 aa) (S11 Desk). The repeat models of those proteins are various, however clusters enriched in Ok, E, and I (cluster 10 and 11) have been significantly frequent (6/18). Though it’s doable that these are wrongly predicted genes in intergenic areas, they might even be de novo repeat peptides. Their existence as actual proteins is supported by the remark that they possess a begin codon (or different begin codon), the TR models are divisible by three and thus introduce aaTRs, and by the truth that 4 have sign peptides and 4 have practical annotations (linked to apolipoprotein, proline-rich domains, and a glycoprotein area).

To analyze which capabilities aaTR-proteins have, and if functionally associated proteins possess comparable aaTRs, we carried out protein household clustering of 11,995 Borg proteins. Briefly, we clustered proteins utilizing the quick and delicate protein sequence looking out software program MMseqs2 [18] in an all-versus-all strategy to outline protein subclusters based mostly on amino acid similarities. Based mostly on the alignments of the subfamily members, HMMs have been generated for every subfamily utilizing HHblits [19]. These HMMs have been then functionally annotated by an HMM-HMM comparability with the PFAM database utilizing HHSearch [20]. This resulted in 85% of Borg proteins being grouped into 1,890 subfamilies and 80% (172/215) of the aaTR-proteins clustered into 112 subfamilies (S6 Desk). Based mostly on the annotations for the person protein members of every subfamily and the annotation of the HMM of the subfamily, protein subfamilies have been manually grouped when it comes to operate. The practical panorama of the subfamilies ranged from carbon metabolism (18 proteins), cell and protein structure and scaffolding (9), nucleotide processing (15), transcription-associated proteins (8), redox (8), signaling (11), transport (3), stress response (2), to protein processing (1) (Desk 2).

Desk 2. Useful annotations for protein subfamilies with aaTR-bearing protein members.

Proteins have been manually positioned into practical classes based mostly on the pfam annotation of the subfamily. Single aaTR models are listed in addition to through which aaTR cluster they fall. Some aaTRs didn’t fall into clusters (n.c., no cluster), and a few proteins have two or extra aaTRs, which fall into one or two aaTR clusters.

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Screening the aaTR-proteins with the eukaryotic linear motif (ELM) useful resource for practical websites in proteins (http://elm.eu.org/) unmasked that the aaTRs inside them have similarity to a plethora of various brief linear motifs (SLiMs). SLiMs are composed of three to 10 consecutive amino acids [21], that are utilized by eukaryotic cells as cleavage websites, degradation websites, docking websites, ligand binding websites, posttranslational modification websites, and focusing on websites [22]. We discovered that aaTRs from the identical aaTR cluster or associated aaTR clusters typically had matching practical predictions (see examples in S7 Desk).

Fifteen protein subfamilies have been enriched in aaTR-proteins, which included subfamilies functionally annotated as transmembrane phosphatases, ribonucleoproteins, phosphoesterases, zinc-ribbon proteins, and DNA-binding proteins; the opposite subfamilies had no practical annotations (S6 Desk). Members of the identical protein subfamily typically had comparable aaTRs. For instance, a subfamily of DNA binding proteins (subfam0897) solely includes aaTR-bearing members, all of which have aaTRs which might be distinctive in nucleotide sequence (S8 Fig), but of the identical or associated repeat clusters (Fig 6B). These aaTRs type a predicted coil construction or an IDR and resemble SLiMs that play a job in ligand binding, degradation, and focusing on (S7 Desk). Equally, subfam1609 includes eight members, 5 of that are aaTR-proteins, and, regardless of all being solely distant homologues (highest aa identification is 67%), the aaTRs are encoded by distinctive nucleotide TR models (S8 Fig) however belong to the identical aaTR cluster (SVG/IQ), which corresponds to predicted modification (phosphorylation) and ligand-binding websites (Fig 6B and S7 Desk).

A number of functionally associated however phylogenetically unrelated proteins which might be accountable for cell wall structure (PEGA and S-layer) and ornament (glycosyltransferases and glycosyl hydrolases) have aaTRs. The aaTRs of the PEGA proteins resemble predicted ligand binding, docking, and modification (phosphorylation) websites, and the aaTRs of the S-layer resemble proteolysis-initiating degrons [23]. The aaTRs of glycosyl hydrolases resemble modification and ligand binding websites, and the aaTRs of glycosyl transferases resemble degrons (S7 Desk). Some Borgs additionally possess an aaTR in tubulins, that are proteins required for cell division [24]. These aaTRs resemble SLiMs which might be potential docking and cleavage websites and/or provoke proteasomal degradation. Importantly, these SliM-bearing aaTRs are absent in non-Borg homologues.

Most Borgs encode Sm ribonucleoproteins, that are archaeal homologues of bacterial Hfq and eukaryotic Sm/Sm-like (Lsm) proteins. These proteins are implicated in versatile capabilities equivalent to RNA-processing and stability, and the protein monomers type a secure hexameric or heptameric ring-shaped particle [25,26]. We discovered 19 Borg Sm ribonucleoproteins (S12 Desk), 5 possess aaTRs, and one further sequence from Gray Borg has a near-perfect aaTR. The aaTRs are at all times positioned on the N-terminus, preserving the conserved Sm1 and Sm2 RNA-binding motifs (S9A Fig). The aaTR models include 4, 8, 12, or 17 amino acids, have the identical aa character, and are predicted SLiMs that facilitate docking or resemble degrons (S9B Fig and S12 Desk). An preliminary homology-based structural search of the aaTR-Sm from Black Borg recognized the bacterial Hfq of Pseudomonas aeruginosa (PDB: 4MML, aa identification: 26%) that kinds a homohexameric ring construction. On account of no alignable template within the database for the aaTR, the mannequin didn’t predict a construction of this N-terminal area. Reworking with AlphaFold2 predicted the construction of the Sm core that shaped a hexameric ring with lengthy loops extending on the distal aspect of the protein (Fig 7). This unstructured area corresponds to the aaTR area and matches the prediction of MobiDBLite [27] and IUPred3 [28] that the aaTR is an IDR. Modeling of the opposite 4 aaTR-Sm proteins additionally confirmed N-terminal unstructured extensions similar to the aaTRs, which have been equally predicted IDRs (S9C Fig).

Fig 7. Predicted constructions of aaTR-bearing ribonucleoproteins and multiheme cytochromes.

(A) Sm ribonucleoprotein from Black Borg was superimposed on Sm from M. jannaschii (blue, PDB: 4X9D with UMP RNA + ions, magenta). (B) MHC area structure and predicted constructions. aaTR areas in predicted constructions are highlighted in purple, and amino acid sequence of every aaTR unit is proven in brackets beneath every construction. Buildings have been predicted with AlphaFold2.

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All Borgs encode MHCs, that are significantly essential and plentiful in Methanoperedens as they mediate the ultimate electron switch from methane metabolism to an exterior electron acceptor [29]. We discovered 14 MHCs with aaTRs in Borg genomes. All of those are predicted to be positioned extracellularly, some possess a membrane anchor, they usually vary from 20.5 kDa (190 aa) to 137.5 kDa (1,293 aa) and include as much as 30 heme binding websites (Fig 7). The proteins are thus clearly distinct in sequence and area structure. The aaTRs are positioned at totally different websites within the polypeptides however by no means disrupt present practical domains. But remarkably, the aaTRs belong to equivalent or comparable repeat clusters which might be persistently enriched in T and P and resemble ligand binding, docking, and modification websites (S13 Desk). The aaTRs are principally IDRs, that are predicted to type unstructured extensions that protrude from the folded protein core.

There’s a area in all full Borg genomes that could be a hotspot for TRs with as much as 5 aaTR-bearing proteins (Fig 8A). It features a gene encoding subfam1773, which we consult with as cell envelope integrity protein TolA. Finest blastp and structural hits are TolA from, e.g., the pathogenic bacterium Leptospira sarikeiensis (48% aa identification with WP_167882360) and YgfJ from the pathogen Salmonella typhimurium (PDB: 2JRP). Eight TolA proteins have distinctive aaTRs, and a few carry further aaTR models shared by different Borgs (e.g., Ochre Borg repeat models are present in Rose Borg and Purple Borg) (Fig 8B). These aaTRs are comparable in amino acid composition and they’re predominantly predicted degradation, docking, and ligand binding websites (S6 and S7 Tables). The areas encode two different conserved protein subfamilies with aaTR-bearing members: subfam0649 missing practical annotation and a subfamily of zinc-ribbon proteins (subfam0108), which normally type interplay modules with nucleic acids, proteins, or metabolites. The subfam0108 proteins possess seven distinct aaTR models, six of which fall into the identical repeat cluster (S6 and S7 Tables). Further aaTR-bearing proteins in the identical context are a glycogen synthase/glycosyl transferase (subfam0184) in Black Borg and Inexperienced Borg and proteins of unknown operate (subfam1382) in Lilac Borg and Orange Borg, and a hypothetical protein in Inexperienced Borg.

Fig 8. A conserved genetic area is a hotspot for tandem repeats.

(A) Gene cluster alignment of a conserved area in all Borg genomes that encompasses TolA. The alignment is predicated on amino acid identification and was generated with clinker [48]. (B) Most TolA homologues have at the very least one aaTR area. The aaTR models are depicted as arrays beneath every sequence, and areas with two aaTR models solely are proven as properly.

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