Strolling Toward New Concepts

Abstract

For more than four decades now, I have been studying how genetic information is transformed into protein-based cellular functions. This has included investigations into the mechanisms supporting cellular localization of proteins, disulfide bond formation, quality control of membranes, and translation. I tried to extract new principles and concepts that are universal among living organisms from our observations of Escherichia coli. While I wanted to distill complex phenomena into basic principles, I also tried not to overlook any serendipitous observations. In the first part of this article, I describe personal experiences during my studies of the Sec pathway, which have centered on the SecY translocon. In the second part, I summarize my views of the recent revival of translation studies, which has given rise to the concept that nonuniform polypeptide chain elongation is relevant for the subsequent fates of newly synthesized proteins. Our studies of a class of regulatory nascent polypeptides advance this concept by showing that the dynamic behaviors of the extraribosomal part of the nascent chain affect the ongoing translation process. Vibrant and regulated molecular interactions involving the ribosome, mRNA, and nascent polypeptidyl-tRNA are based, at least partly, on their autonomously interacting properties.

Polymorphism at four-fold degenerate site, but not at the intergenic regions, explains nucleotide compositional strand asymmetry in bacteria

“…In case of nearly neutral nature, polymorphism patterns of different amino acids at FFS and at IRs are expected to be similar considering the role of context dependent mutation being minimal. The assumption of nearly neutral nature of FFS could be questioned based on the findings of earlier work in the areas of cotranslational protein folding, selection on synonymous codons and ribosome mediated gene regulation (Satapathy et al 2014;Sohmen et al 2015;Ray and Goswami 2016;Ito 2016). Moreover, the findings by Charneski et al (2011) support the role of selection for the atypical AT skew in S. aureus, emphasising the role of strand bias gene distribution in compositional skew (Charneski et al 2011).…”