Generalizable strategy to analyze domains in the context of parent protein architecture: A CheW case study

Abstract

Domains are the three-dimensional building blocks of proteins. An individual domain can be found in a variety of protein architectures that perform unique functions and are subject to different evolutionary selective pressures. We describe an approach to evaluate the variability in amino acid sequences of a single domain across architectural contexts. The ability to distinguish the different evolutionary paths of one protein domain can help determine whether existing knowledge about a specific domain will apply to an uncharacterized protein. Such discrimination can lead to insights and hypotheses about function, as well as guide experimental priorities.We developed and tested our approach on CheW-like domains (PF01584), which mediate protein/protein interactions and are difficult to compare experimentally. CheW-like domains occur in CheW scaffolding proteins, CheA kinases, and CheV proteins that regulate bacterial chemotaxis. We chose 16 protein Architectures that included 94% of all CheW-like domains found in nature. Because some Architectures had more than one CheW-like domain, CheW-like domains were divided into 21 distinct Contexts. The CheW-like domain sequences were closely related within most Contexts; however, one Context was subdivided into three Types. The resulting 23 sequence Types coalesced into five or six Classes of CheW-like domains, which we described in detail.In addition, we created SimpLogo, an innovative method for visualizing amino acid composition across large sets of multiple sequence alignments of arbitrary length. SimpLogo offers substantial advantages over standard sequence logos for comparison and analysis of related protein sequences. The R package for SimpLogo is freely available.

Analysis of CheW-like domains provides insights into organization of prokaryotic chemotaxis systems

“…We previously extracted all proteins that contained CheW-like domains and belonged to the 16 Architectures (Figure 2) that account for ∼94% of CheW-like domains within the Representative Proteome 35 (RP35) dataset. 36 Using the same dataset, we extracted the remaining known chemotaxis proteins (with the exception of CheY), resulting in components from 1887 distinct proteomes. MCPs were classified by number of heptad repeats, 49 whereas CheB, CheC (including closely related CheX 50 ), CheD, CheR, and CheZ proteins were assigned to the chemotaxis system categories of Wuichet and Zhulin.…”

“…31 ). CheW.IB linked with CheA.I and CheA.II (the two most common CheA Architectures 36 ) in Figure 5. CheW.IB also connected to multiple types of MCPs in Figure 5.…”

“…The CheW.IA Type comprises Class 6 of CheW-like domains and makes up ∼20% of CheW.I proteins. 36 CheW.IA is subtly distinguishable from CheW.IB and CheV.I Types of CheW-like domains ( Class 1) by some (but not all) methods of sequence analysis. 36 In Figure 5, CheW.IA made direct connections to various chemoreceptors, but not to any CheA proteins (i.e., phyletic coupling of CheW.IA was stronger to MCPs than to CheA-lineage proteins).…”

“…A recent companion paper describes our classification (Figure 1) of the numerous architectural contexts of CheW-like domains and the implications thereof. 36 Nearly all (∼94%) CheW-like domains are encompassed by 16 distinct Architectures (Figure 2). Because certain Architectures include multiple CheW-like domains, there are 21 major Contexts for CheW-like domains.…”

“…The CheW.I Architecture splits into three Types 36. b From36 . The two CheW-like domains in CheA.V and CheA.VI Architectures belong to different Classes.…”