Abstract:
BACKGROUND:The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. RESULTS:This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. CONCLUSION:This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Pal LR,Guda Cdoi
10.1186/1471-2148-6-91subject
Has Abstractpub_date
2006-11-07 00:00:00pages
91issn
1471-2148pii
1471-2148-6-91journal_volume
6pub_type
杂志文章abstract:BACKGROUND:There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic dif...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-28
更新日期:2008-01-28 00:00:00
abstract:BACKGROUND:The multiplicity or loss of the vitellogenin (vtg) gene family in vertebrates has been argued to have broad implications for the mode of reproduction (placental or non-placental), cleavage pattern (meroblastic or holoblastic) and character of the egg (pelagic or benthic). Earlier proposals for the existence ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-2
更新日期:2009-01-05 00:00:00
abstract:BACKGROUND:The acquisition of complex transcriptional regulatory abilities and epigenetic machinery facilitated the transition of the ancestor of apicomplexans from a free-living organism to an obligate parasite. The ability to control sophisticated gene expression patterns enabled these ancient organisms to evolve sev...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-37
更新日期:2013-02-11 00:00:00
abstract:BACKGROUND:Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes t...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-66
更新日期:2008-02-26 00:00:00
abstract:BACKGROUND:Many species of social insects have large-scale mating and dispersal flights and their populations are therefore often relatively homogenous. In contrast, dispersal on the wing appears to be uncommon in most species of the ant genus Cardiocondyla, because its males are wingless and the winged queens mate in ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1448-6
更新日期:2019-06-06 00:00:00
abstract:BACKGROUND:Timing the origin of human malarias has been a focus of great interest. Previous studies on the mitochondrial genome concluded that Plasmodium in primates, including those parasitic to humans, radiated relatively recently during a process where host switches were common. Those investigations, however, assume...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-299
更新日期:2011-10-12 00:00:00
abstract:BACKGROUND:Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of o...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-85
更新日期:2010-03-29 00:00:00
abstract:BACKGROUND:Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphologi...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-020-01639-y
更新日期:2020-06-26 00:00:00
abstract:BACKGROUND:Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0362-9
更新日期:2015-06-11 00:00:00
abstract:BACKGROUND:In plants the hormone cytokinin is perceived by members of a small cytokinin receptor family, which are hybrid sensor histidine kinases. While the immediate downstream signaling pathway is well characterized, the domain of the receptor responsible for ligand binding and which residues are involved in this pr...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-62
更新日期:2007-04-17 00:00:00
abstract:BACKGROUND:The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0806-x
更新日期:2016-10-28 00:00:00
abstract:BACKGROUND:Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-020-01653-0
更新日期:2020-07-16 00:00:00
abstract:BACKGROUND:Nuclear progesterone receptor (nPR) is an evolutionary innovation in vertebrates that mediates genomic responses to progesterone. Vertebrates also respond to progesterone via membrane progesterone receptors (mPRs) or membrane associated progesterone receptors (MAPRs) through rapid nongenomic mechanisms. Lamp...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1463-7
更新日期:2019-07-01 00:00:00
abstract:BACKGROUND:Raphidioptera (snakeflies) is a holometabolous order of the superorder Neuropterida characterized by the narrowly elongate adult prothorax and the long female ovipositor. Mesozoic snakeflies were markedly more diverse than the modern ones are. However, the evolutionary history of Raphidioptera is largely une...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-14-84
更新日期:2014-04-18 00:00:00
abstract:BACKGROUND:Dispersal is often associated with a suite of phenotypic traits that might reduce dispersal costs, but can be energetically costly themselves outside dispersal. Hence, dispersing and philopatric individuals might differ throughout their life cycle in their management of energy production. Because higher ener...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0697-x
更新日期:2016-06-14 00:00:00
abstract:BACKGROUND:A single measles vaccination provides lifelong protection. No antigenic variants that escape immunity have been observed. By contrast, influenza continually evolves new antigenic variants, and the vaccine has to be updated frequently with new strains. Both measles and influenza are RNA viruses with high muta...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-229
更新日期:2007-11-15 00:00:00
abstract:BACKGROUND:Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered a...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-149
更新日期:2012-08-20 00:00:00
abstract:BACKGROUND:Cardiolipin (CL) is an important component in mitochondrial inner and bacterial membranes. Its appearance in these two biomembranes has been considered as evidence of the endosymbiotic origin of mitochondria. But CL was reported to be synthesized through two distinct enzymes--CLS_cap and CLS_pld in eukaryote...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-32
更新日期:2012-03-13 00:00:00
abstract:BACKGROUND:Many species with sexual and asexual variants show a pattern of geographic parthenogenesis where asexuals have broader and higher-latitude distribution than sexuals. Because sexual reproduction is often considered a costly evolutionary strategy that is advantageous in the face of selection by coevolving pest...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-23
更新日期:2013-01-28 00:00:00
abstract:BACKGROUND:Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0473-3
更新日期:2015-09-16 00:00:00
abstract:BACKGROUND:Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccat...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-5-57
更新日期:2005-10-20 00:00:00
abstract:BACKGROUND:Recent studies have revealed an unexpected diversity of domain architecture among FcR-like receptors that presumably fulfill regulatory functions in the immune system. Different species of mammals, as well as chicken and catfish have been found to possess strikingly different sets of these receptors. To bett...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-148
更新日期:2008-05-16 00:00:00
abstract:BACKGROUND:Phylactolaemata is commonly regarded the earliest branch within Bryozoa and thus the sister group to the other bryozoan taxa, Cyclostomata and Gymnolaemata. Therefore, the taxon is important for the reconstruction of the bryozoan morphological ground pattern. In this study the myoanatomy of Pectinatella magn...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-017-1068-y
更新日期:2017-11-07 00:00:00
abstract:BACKGROUND:Any DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions. However, it is important to discriminate between the effect of mu...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-1-13
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:Dynactin is a large multisubunit protein complex that enhances the processivity of cytoplasmic dynein and acts as an adapter between dynein and the cargo. It is composed of eleven different polypeptides of which eight are unique to this complex, namely dynactin1 (p150(Glued)), dynactin2 (p50 or dynamitin), d...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-95
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:The hypothesis of an RNA-based origin of life, known as the "RNA world", is strongly affected by the hostile environmental conditions probably present in the early Earth. In particular, strong UV and X-ray radiations could have been a major obstacle to the formation and evolution of the first biomolecules. I...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-S2-S2
更新日期:2007-08-16 00:00:00
abstract:BACKGROUND:The ability of an immune system to remember pathogens improves the chance of the host to survive a second exposure to the same pathogen. This immunological memory has evolved in response to the pathogen environment of the hosts. In vertebrates, the memory of previous infection is physiologically accomplished...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-380
更新日期:2010-12-08 00:00:00
abstract:BACKGROUND:In gnathostomes, chemosensory receptors (CR) expressed in olfactory epithelia are encoded by evolutionarily dynamic gene families encoding odorant receptors (OR), trace amine-associated receptors (TAAR), V1Rs and V2Rs. A limited number of OR-like sequences have been found in invertebrate chordate genomes. Wh...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-180
更新日期:2009-07-31 00:00:00
abstract:BACKGROUND:The rate of molecular evolution varies widely between proteins, both within and among lineages. To what extent is this variation influenced by genome-wide, lineage-specific effects? To answer this question, we assess the rate variation between insect lineages for a large number of orthologous genes. RESULTS...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-6-7
更新日期:2006-01-25 00:00:00
abstract:BACKGROUND:Remipedia were initially seen as a primitive taxon within Pancrustacea based on characters considered ancestral, such as the homonomously segmented trunk. Meanwhile, several morphological and molecular studies proposed a more derived position of Remipedia within Pancrustacea, including a sister group relatio...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-119
更新日期:2013-06-10 00:00:00