RE: Pseudogenes and mobile elements

From: Alexanian, Moorad <alexanian@uncw.edu>
Date: Thu Oct 06 2005 - 15:39:42 EDT

Is common ancestry analogous to the unification of forces in particle physics? Why do conscious, rational beings find these notions so appealing? Heisenberg ascribed this to the idea of one God.

 
Moorad

________________________________

From: asa-owner@lists.calvin.edu on behalf of Charles Austerberry
Sent: Thu 10/6/2005 2:43 PM
To: asa@lists.calvin.edu
Subject: Pseudogenes and mobile elements

Cornelius and Preston are discussing an interesting topic (transposable elements and pseudogenes). Those working in comparative genomics (including evangelical Christians such as Francis Collins) are most familiar with the subject, and they have concluded that common ancestry is clearly supported by this type of data.

Cornelius has made some valuable contributions in regards to understanding Darwin's metaphysical views, but when it comes to molecular genetics, Preston appears to be more familiar with the data.

A related question is: can transposable elements and/or pseudogenes mutate in ways that (re)generate functional genes? Perhaps. Below are references to a couple of papers, with brief summaries.

God be with you.

Yours in Christ,

Chuck Austerberry
*****************************
Two Publications of Interest
 
Emergence of Talanin protein associated with human uric acid nephrolithiasis in the Hominidae lineage. Gianfrancesco et. al. (2004), Gene Volume 339, pp. 131-138.

* In most mammals, uricase degrades uric acid to allantoin.
* The uricase gene exists as non-functional pseudogene in hominoids (apes and humans).
* Primates that still have a functional copy express it at low levels compared to rodents and rabbits, due to mutations in the upstream regulatory region of the gene.
* Various hypotheses exist for why some animals fare better with little or no uricase, and the resulting high levels of uric acid (10x the uric acid levels found in rodents).
* A nonsense mutation in codon 33 is found in orangutans, gorillas, chimpanzees, and humans, so it probably occurred in a common ancestor 12-24 million years ago.
* Another nonsense mutation occurred subsequent to the divergence between orangutans and the others (gorilla, chimp, and humans) because it's not found in orangutans but it is in the other three.
* A disease called uric acid nephrolithiasis (UAN) results if the alternative means humans use to limit uric acid levels (to "only" 10x that in rodents) fail.
* Gianfrancesco et al. have identified a gene, Talanin, where mutations are associated with some cases of UAN.
* This gene appears to have evolved from noncoding genomic sequences found at the same location in the genomes of primates that do have uricase activity.

Coding sequences of functioning human genes derived entirely from mobile element sequences. Britten (2004), Proceedings of the National Academy of Sciences (U.S.A.) Volume 101, pp. 16825-16830.
 
About 45% of the human genome is derived from ancient mobile elements.

* 2.8% consists of transposable elements similar to those common in invertebrates and plants.(The DNA-mediated, rather than reverse-transcription-mediated, transposons). There are about 300,000 of these in the human genome.
* 42.2% consists of "retroelements," which generate new copies via RNA intermediates that are "reverse transcribed" into DNA. These new DNA copies of retroelement RNA rarely leave a chromosome once integrated.

        * About 300,000 of these are human endogenous retroviruses (HERVs).
        * About 2.4 million of the human retroelements now lack most viral-like sequences, but they can still make copies of what they have left.

                * Long Interspersed Elements (LINEs) can still make reverse transcriptase.
                * Short Interspersed Elements (SINEs) depend upon LINEs or HERVs to provide the reverse transcriptase that inserts new DNA copies of SINE RNAs in new genomic locations.

         Some LINEs are very ancient, predating our lineage's split from the lineage leading to rodents. Others are more recent. Most of our SINEs originated more recently too (rodents have their own SINEs, distinct from primate SINEs).
        
        Some important proteins encoded by genes apparently derived from retroelements include Syncytin (functions in the human placenta), GTF2IRD2 (a transcription factor), and AD7C (a neuronal thread protein).

        ******************************************************
        Charles F. Austerberry, Ph.D.
        Assistant Professor of Biology
        Creighton University
        e-mail: cfauster@creighton.edu
        Nebraska Religious Coalition for Science Education
        http <http://nrcse.creighton.edu> ://nrcse.creighton.edu <http://nrcse.creighton.edu>
Received on Thu Oct 6 15:43:24 2005

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