MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

Liu, Yong-Chao; Schmidt, Bertil; Maskell, Douglas L.

doi:10.1093/bioinformatics/btq338

Cited by 215 publications

(184 citation statements)

References 37 publications

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“…Orthologs of the Rubisco family were identified by BLAST search based on the amino acid sequences of groups IA and IB Rubisco in Synechococcus elongatus and group IV Rubisco in Baccillus , using the NCBI BLAST Tool (Altschul, Gish, Miller, Myers, & Lipman, 1990). Using 81 curated sequences, multiple sequence alignments were inferred using MSAProbs (Liu, Schmidt, & Maskell, 2010) and MUSCLE (Edgar, 2004) with the default settings. Both of these alignments were best‐fit by the PROTCATWAG model (Lartillot & Philippe, 2004; Le & Gascuel, 2008), with model fitness assessed using the Akaike information criterion (Abascal, Zardoya, & Posada, 2005).…”

Section: Methodsmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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Ribulose 1,5‐bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen‐sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem‐bearing, oxygen‐evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen‐sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

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Section: Methodsmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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“…Sequences within each putative ortholog were further clustered so that a single transcript represented each ortholog from each species. Transcripts were translated, and amino acid sequences were aligned with MSAprobs (84). Alignments were back-translated to the original nucleic acids with RevTrans (85) and trimmed of poorly aligned regions using Gblocks (86).…”

Section: Methodsmentioning

confidence: 99%

Rapid molecular evolution across amniotes of the IIS/TOR network

McGaugh

Bronikowski

Kuo

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile-and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub-or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.insulin signaling | insulin growth factor | molecular evolution | rapamycin T he last 20 y has provided overwhelming support that the insulin-and insulin-like signaling/target of rapamycin (IIS/TOR) molecular network responds to stress and nutrients and underlies a wide range of physiological functions (1); cancer, metabolic syndrome, and diabetes (2); and the timing of life events (e.g., growth, maturation, reproduction, and aging) (3). The vertebrate IIS/TOR network consists of peptide hormones, binding proteins that regulate hormone bioavailability, and cell membrane receptors (hereafter, extracellular proteins of the IIS/TOR network) that induce an intracellular signaling cascade (hereafter, intracellular proteins of the IIS/TOR network) to stimulate cell proliferation, survival, and metabolism (Fig. S1). The core intracellular signal transduction genes in this network are largely conserved across deep phylogenetic time (4, 5). In contrast, genes encoding the IIS/TOR extracellular network have diverged in the vertebrate lineage (6-8) and may have variable roles among taxa (9, 10). Despite its central rol...

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“…Differents refinement techniques have been developed [16]. Among multiple sequence alignment algorithms using progressive approach, we mention CLUSTALW [17], T-COFFEE [18], MAFFT [7], MUSCLE [6] ProbCons [8], Gramalign [9], MSAProbs [10], Motalign [19], GLProbs [12] and Clustal Omega [20].…”

Section: State Of the Artmentioning

confidence: 99%

Pro-malign: Multiple Sequence Alignment Algorithm using Approached Profile

Mokaddem¹,

Haj²,

Elloumi³

2018

JSW

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Abstract:In this paper, we present a new progressive multiple sequence alignment algorithm called Promalign. Our algorithm introduces the approached profile sequence a new definition of profile that aim to conserve similar residues in the alignment. The approached profile sequence is used to compute a new distance called approached profile distance. We present also a new score function between profiles and a new refinement algorithm. We assess our program Pro-malign on different datasets extracted from different benchmarks of protein sequences and we compare the scores obtained to other scores of the most efficient multiple sequence alignment programs.

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MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

Abstract: The source code of MSAProbs, written in C++, is freely and publicly available from http://msaprobs.sourceforge.net.

Cited by 215 publications

References 37 publications

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Rapid molecular evolution across amniotes of the IIS/TOR network

Pro-malign: Multiple Sequence Alignment Algorithm using Approached Profile

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